Research workbench
Crystal structure of D26A mutant upps in complex with mg, ipp and fspp
Analyse Crystal structure of D26A mutant upps in complex with mg, ipp and fspp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X08
- Type
- protein
- Length
- 228 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Undecaprenyl pyrophosphate synthetase
- EC
- 2.5.1.31
- UniProt
- P60472
- Ligands
- FPS, IPE
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) | protein | 228 | 50% helix, 15% strand | P60472 |
Ligands and binding sites
- FPS · S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen thiodiphosphate · ligand · 2 copies · chains A
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.80 | 0.87 | 59 | FPS, IPE |
| 2 | 92 | 0.34 | 0.74 | 18 | empty |
| 3 | 55 | 0.33 | 0.78 | 16 | empty |
Compared structures
- 1X08 · Crystal structure of D26A mutant UPPs in complex with Mg, IPP and FsPP · the same entry in another collection · chain A against A, TM-score 1.00
- P60472 · AlphaFold monomer V2.0 prediction for DITRANS,POLYCIS-undecaprenyl- diphosphate synthase… · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P60472
- Elsewhere: RCSB PDB 1X08 · PDBe 1X08 · UniProt P60472
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